Afton was free before Glitchtrap and has been in charge of Neo-FazEnt from the beginning.

[Amazingspore1026]

Let me explain.
So there's no doubt in anyone's mind that William Afton has a connection to the higher-ups, as Security Breach messages involving the unqualified Vanessa being hired as head security guard because a higher-up vouched for her have shown.
Then there's the fact that the company itself appears to have some awareness of what Glitchtrap is intending to do,("Fazbear Entertainment is not responsible for digital consciousness transfers", says HandUnit quickly in the beginning. Ah yes, wasn't HandUnit William Afton's invention when he created Circus Baby Entertainment and Rental?)
Now the idea has been brought up by MatPat-what if this is just someone who is Team William, not the man himself?
I doubt this because of two things:
One, the circuits that introduce Glitchtrap to the game are critical to this mystery person's plan, yes. William has always been a lone wolf, if he had a partner in crime, then why would they take so long?
Two, if William had a friend on the outside, he would probably have ensured they would have quick access to everything they needed to revive him if that were the case? Why only hear from them now? Why have an ally of William who's supposedly been with him for a while only NOW make an appearance?

It's possible that William could found the company without any proper body for himself-in the modern world with internet access, he could theoretically do everything he needed to start his new business without making a single personal experience!